Note
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Counting gaps per sequence
We have several different ways of counting sequence gaps, and of visualising the results. By default, the count_gaps_per_seq() method returns a matrix of counts without the ability to visualise the results. When setting the argument unique=True, the counts are for gaps uniquely induced by each sequence. This can be a useful indicator of highly divergent sequences.
from cogent3 import load_aligned_seqs
aln = load_aligned_seqs('../../data/brca1.fasta', moltype='dna')
counts = aln.count_gaps_per_seq(unique=True)
counts
| FlyingFox |
DogFaced |
FreeTaile |
LittleBro |
TombBat |
RoundEare |
FalseVamp |
| 0 |
0 |
0 |
0 |
0 |
0 |
0 |
| FlyingFox |
LeafNose |
Horse |
Rhino |
Pangolin |
Cat |
Dog |
Llama |
Pig |
Cow |
Hippo |
| 0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
| FlyingFox |
SpermWhale |
HumpbackW |
Mole |
Hedgehog |
TreeShrew |
FlyingLem |
Galago |
| 0 |
0 |
0 |
0 |
0 |
3 |
0 |
3 |
| FlyingFox |
HowlerMon |
Rhesus |
Orangutan |
Gorilla |
Human |
Chimpanzee |
Jackrabbit |
| 0 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
| FlyingFox |
FlyingSqu |
OldWorld |
Mouse |
Rat |
NineBande |
HairyArma |
Anteater |
| 0 |
57 |
0 |
0 |
0 |
0 |
0 |
0 |
| FlyingFox |
Sloth |
Dugong |
Manatee |
AfricanEl |
AsianElep |
RockHyrax |
TreeHyrax |
| 0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
| FlyingFox |
Aardvark |
GoldenMol |
Madagascar |
Tenrec |
LesserEle |
GiantElep |
| 0 |
0 |
0 |
0 |
6 |
0 |
6 |
| FlyingFox |
Caenolest |
Phascogale |
Wombat |
Bandicoot |
| 0 |
0 |
0 |
0 |
0 |
Plotting counts of unique gaps
There are three plot types supported. In all cases, placing the mouse pointer over a data point will show hover text with the sequence name.
Displaying unique gaps as a bar chart
counts = aln.count_gaps_per_seq(unique=True, drawable='bar')
counts.show(width=500)
Displaying unique gaps as a violin plot
counts = aln.count_gaps_per_seq(unique=True, drawable='violin')
counts.show(width=300, height=500)
Displaying unique gaps as a box plot
counts = aln.count_gaps_per_seq(unique=True, drawable='box')
counts.show(width=300, height=500)
Total running time of the script: ( 0 minutes 0.599 seconds)
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